The UK Animal and Plant Health Agency (APHA) recently published a review of its scientific accomplishments throughout 2021. The report highlights certain developments that impact food safety regarding whole genome sequencing (WGS) and antimicrobial resistance (AMR).
APHA has reported an ongoing transition from conventional serotyping to WGS-based typing of Salmonella. In a single test, the new pipeline can differentiate between wild Salmonella isolates and live vaccine strains that are licensed in the UK for use in poultry and pigs. A full-throughput parallel trial was successfully completed, and preparations for launching the new WGS-based serotyping service are underway. WGS for Salmonella aligns with testing of human and food isolates by public health authorities in England and Scotland, and by the European Salmonella Reference Laboratory. APHA states that WGS is being used to detect outbreaks in real time, and the agency predicts that WGS could replace most AMR testing, phage typing, and molecular testing in the future.